Molecular Plant Breeding 2024, Vol.15, No.5, 259-268 http://genbreedpublisher.com/index.php/mpb 260 This study aims to evaluate the impact of marker-assisted selection on soybean breeding efficiency; assess the current state of soybean breeding and the limitations of traditional methods; review the advancements in MAS and its application in soybean breeding; analyze the integration of MAS with other modern breeding technologies and provide recommendations for optimizing MAS to achieve higher breeding efficiency and better trait improvement. 2 Basics of Marker-Assisted Selection (MAS) 2.1 Definition and principles of marker-assisted selection Marker-assisted selection (MAS) is a modern plant breeding technique that utilizes molecular markers to select plants with desirable traits. Unlike conventional breeding, which relies heavily on phenotypic selection, MAS leverages genetic information to make more precise and efficient selections. The principle behind MAS is to identify and use markers- specific DNA sequences linked to traits of interest- to track the presence of these traits in breeding populations. This method allows for the early and accurate selection of plants with desired characteristics, thereby accelerating the breeding process and improving the efficiency of developing new cultivars (Babu et al., 2004; Torres et al., 2010; Boopathi, 2020). 2.2 Types of molecular markers used in MAS Several types of molecular markers are employed in MAS, each with its own advantages and applications. Simple sequence repeats (SSRs) also known as microsatellites, SSRs are short, repetitive DNA sequences that are highly polymorphic. They are widely used due to their high level of variability, co-dominant inheritance, and ease of detection (Santana et al., 2014). Single nucleotide polymorphisms (SNPs) are single base-pair variations in the DNA sequence. They are the most abundant type of genetic variation and can be efficiently detected using high-throughput genotyping technologies. SNPs are particularly useful for fine mapping and association studies (Babu et al., 2004; He et al., 2014). Genotyping-by-sequencing (GBS) is a next-generation sequencing approach that combines marker discovery and genotyping. It involves sequencing a reduced representation of the genome, which allows for the identification and genotyping of thousands of SNPs simultaneously. This method is cost-effective and suitable for large-scale breeding programs (He et al., 2014). 2.3 Advantages of MAS over conventional breeding techniques MAS offers several advantages over traditional breeding methods. MAS allows for the selection of desirable traits at the seedling stage, reducing the time and resources needed for phenotypic evaluations over multiple generations (Torres et al., 2010; Boopathi, 2020). By using molecular markers linked to specific traits, MAS enables more accurate selection, reducing the likelihood of retaining undesirable traits and increasing the probability of achieving breeding goals (Babu et al., 2004; Sebastian et al., 2010). Although the initial setup for MAS can be expensive, the overall cost of breeding programs can be reduced due to fewer field trials and faster development of new cultivars (He et al., 2014). MAS is particularly useful for traits that are difficult to select phenotypically, such as disease resistance, drought tolerance, and other polygenic traits. It allows breeders to combine multiple desirable traits more effectively (Torres et al., 2010; Santana et al., 2014). 3 Key Traits Targeted in Soybean Breeding Using MAS 3.1 Yield improvement Yield improvement is a primary focus in soybean breeding programs utilizing marker-assisted selection (MAS). The identification and utilization of quantitative trait loci (QTL) associated with grain yield have shown promising results. For instance, a study on elite soybean cultivars demonstrated that context-specific MAS (CSM) could effectively detect yield QTL within specific genetic and environmental contexts. This approach led to statistically significant yield gains of up to 5.8% in selected sublines, with some improved sublines being released as new cultivars (Sebastian et al., 2010). Despite the complexity of yield as a trait, advancements in genotyping technologies and the integration of MAS have facilitated the selection of genotypes with superior agronomic performance (Francia et al., 2005). 3.2 Resistance to biotic stresses (pests and diseases) Breeding for resistance to biotic stresses, such as pests and diseases, is another critical area where MAS has been effectively applied. The use of molecular markers linked to resistance genes has enabled the rapid deployment of
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